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Diet of a rare herbivore based on DNA metabarcoding of feces: Selection, seasonality, and survival

June 30, 2020

In herbivores, survival and reproduction are influenced by quality and quantity of forage, and hence, diet and foraging behavior are the foundation of an herbivore's life history strategy. Given the importance of diet to most herbivores, it is imperative that we know the species of plants they prefer, especially for herbivorous species that are at risk for extinction. However, it is often difficult to identify the diet of small herbivores because: (a) They are difficult to observe, (b) collecting stomach contents requires sacrificing animals, and (c) microhistology requires accurately identifying taxa from partially digested plant fragments and likely overemphasizes less-digestible taxa. The northern Idaho ground squirrel (Urocitellus brunneus) is federally threatened in the United States under the Endangered Species Act. We used DNA metabarcoding techniques to identify the diet of 188 squirrels at 11 study sites from fecal samples. We identified 42 families, 126 genera, and 120 species of plants in the squirrel's diet. Our use of three gene regions was beneficial because reliance on only one gene region (e.g., only trnL) would have caused us to miss >30% of the taxa in their diet. Northern Idaho ground squirrel diet differed between spring and summer, frequency of many plants in the diet differed from their frequency within their foraging areas (evidence of selective foraging), and several plant genera in their diet were associated with survival. Our results suggest that while these squirrels are generalists (they consume a wide variety of plant species), they are also selective and do not eat plants relative to availability. Consumption of particular genera such as Perideridia may be associated with higher overwinter survival.

Publication Year 2020
Title Diet of a rare herbivore based on DNA metabarcoding of feces: Selection, seasonality, and survival
DOI 10.1002/ece3.6488
Authors Amanda R. Goldberg, Courtney J. Conway, David C. Tank, Kimberly R. Andrews, Digpal S. Gour, Lisette P. Waits
Publication Type Article
Publication Subtype Journal Article
Series Title Ecology and Evolution
Index ID 70228412
Record Source USGS Publications Warehouse
USGS Organization Coop Res Unit Seattle